Annotating genomes with massive-scale RNA sequencing

Genome Biol. 2008;9(12):R175. doi: 10.1186/gb-2008-9-12-r175. Epub 2008 Dec 16.

Abstract

Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been made so far to use RNA-Seq for building gene models de novo, that is, in the absence of a set of known genes and/or splicing events. We present G-Mo.R-Se (Gene Modelling using RNA-Seq), an approach aimed at building gene models directly from RNA-Seq and demonstrate its utility on the grapevine genome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Complementary / genetics
  • Genome, Plant*
  • Models, Genetic*
  • RNA, Plant / genetics
  • Sequence Analysis, RNA / economics
  • Sequence Analysis, RNA / methods*
  • Vitis / genetics*

Substances

  • DNA, Complementary
  • RNA, Plant